X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makefile;h=163db6bd0c547f2b73055ab5b4498dbd82ebfea3;hp=5eb8daaab6d8163b1b48852ccef7e21a406b28dc;hb=615301e57c25e241356a9c2380648d117709458d;hpb=bf83aa09a52403a2faf1a1f82489d1e0c8c32283

diff --git a/makefile b/makefile
index 5eb8daa..163db6b 100644
--- a/makefile
+++ b/makefile
@@ -9,11 +9,19 @@
 # Macros
 #
 
-# Optimize to level 3:
-
-CXXFLAGS += -O3
-
+USEMPI ?= no
 64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"5/29/2013\""
+VERSION = "\"1.31.1\""
+FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS = 
+
+# Optimize to level 3:
+CXXFLAGS += -O3 
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#if you are using centos uncomment the following lines
@@ -22,16 +30,19 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#if you are a mac user use the following line
 	TARGET_ARCH += -arch x86_64
 	
+	#if you using cygwin to build Windows the following line
+	#CXX = x86_64-w64-mingw32-g++
+	#CC = x86_64-w64-mingw32-g++
+	#FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
+ 	#TARGET_ARCH += -m64 -static
+
 	#if you are a linux user use the following line
 	#CXXFLAGS += -mtune=native -march=native -m64
 	
-	 CXXFLAGS += -DBIT_VERSION
+	CXXFLAGS += -DBIT_VERSION 
+    FORTRAN_FLAGS = -m64
 endif
 
-MOTHUR_FILES = "\"../release\""
-
-RELEASE_DATE = "\"12/10/2010\""
-VERSION = "\"1.15.0\""
 
 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
 
@@ -40,7 +51,6 @@ else
 	CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
 endif
 
-CYGWIN_BUILD ?= no
 ifeq  ($(strip $(CYGWIN_BUILD)),yes)
     CXXFLAGS += -mno-cygwin
     LDFLAGS += -mno-cygwin 
@@ -49,7 +59,6 @@ endif
 # if you do not want to use the readline library, set this to no.
 # make sure you have the library installed
 
-USEREADLINE ?= yes
 
 ifeq  ($(strip $(USEREADLINE)),yes)
     CXXFLAGS += -DUSE_READLINE
@@ -58,7 +67,6 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -lncurses
 endif
 
-USEMPI ?= yes
 
 ifeq  ($(strip $(USEMPI)),yes)
     CXX = mpic++
@@ -68,7 +76,6 @@ endif
 # if you want to enable reading and writing of compressed files, set to yes.
 # The default is no.  this may only work on unix-like systems, not for windows.
 
-USECOMPRESSION ?= no
 
 ifeq  ($(strip $(USECOMPRESSION)),yes)
   CXXFLAGS += -DUSE_COMPRESSION
@@ -86,11 +93,18 @@ endif
 
 OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
 OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
 
-mothur : $(OBJECTS)
+mothur : fortranSource $(OBJECTS) uchime
 	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
 	
 	strip mothur
+ 
+uchime:
+	cd uchime_src && ./mk && mv uchime .. && cd ..
+	
+fortranSource:
+	${FORTAN_COMPILER} -c $(FORTRAN_FLAGS) *.f
 
 install : mothur
 #	cp mothur ../Release/mothur
@@ -105,4 +119,5 @@ install : mothur
 
 clean :
 	@rm -f $(OBJECTS)
+	@rm -f uchime